Microbial single-cell RNA sequencing for subgingival microbiome

This repository contains metadata and analysis scripts for the single-cell RNA sequencing study of the subgingival microbiome in health control and periodontitis, as presented in Ding et al. [PUBLISHER & YEAR].

For questions regarding this dataset or analysis, please contact:

• Yongcheng Wang (yongcheng@zju.edu.cn)
• Pei-Hui Ding (phding@zju.edu.cn)

Data Availability

Repositary structure

All data files referenced in the analysis scripts (except RDS files) are located in the data/ directory.

Data Access

• Processed data: RDS files, expression matrices, and taxonomy files are available via Figshare, and will be made publicly accessible upon article publication ([LINK]).

• Sequencing data (Genome Sequence Archive):

  • scRNA-seq: CRA023798
  • N.elongata whole-genome sequencing: CRA026826
  • 16S rRNA sequencing: CRA030816

All sequencing data will be made publicly available upon final publication of the article.

Analysis Scripts

Included scripts:

figure2.R: Workflow of QC; clustering; box plot of gene counts; correlation analysis; comparisons between HC and Pd samples.

figure3.R: Clustering; WGCNA; marker gene identification.

figure4.R: Transcriptional alterations in subgingival bacteria under periodontitis.

figure5.R: Functional modules and heterogeneity of N. elongata in HC and Pd groups.

figure6.R: Metabolic signatures of P. gingivalis, P. intermedia, and T. denticola in periodontitis.

Requirement

R packages:

• Seurat (v4.4.0)
• SeuratObject (v5.0.2)
• ggplot2
• data.table
• Hmisc
• monocle
• hdWGCNA
• SingleCellExperiment
• DESeq2
• harmony